Biology subjects

Brand, K.

Publications and source records attributed to Brand, K..

6 recordsLinked to original sources

bioRxiv2026

Single cell in vivo analysis of type I IFN and NK cell-mediated control of B cell infection densities during acute gammaherpesvirus infection

Immunodeficient patients are at risk of severe complications following infection with the human gammaherpesviruses Epstein-Barr virus (EBV) and Kaposis sarcoma-associated herpesvirus (KSHV). Due to the strict host specificity of human gammaherpesviruses, murine gammaherpesvirus 68 (MHV68) is widely used as an in vivo model to study gammaherpesvirus pathogenesis. While type I interferons (IFNs) and natural killer (NK) cells are known to contribute to antiviral defense during MHV68 infection, how these innate immune mechanisms control infection within lymphoid tissues at the level of individual infected cells remains incompletely understood. Here, we used an MHV68-DsRed reporter virus to visualize infected cells in the lymph nodes of wildtype and type I IFN receptor-deficient (Ifnar1-/-) mice by flow cytometry, immunohistochemistry, and two-photon microscopy. We found that type I IFN signaling plays a major role in limiting both local viral infection in draining lymph nodes and systemic dissemination to the spleen during acute infection. In the absence of IFNAR signaling, infected B cells accumulated to higher numbers, including an increased proportion of infected germinal center phenotype B cells, and this was accompanied by enhanced activation of T and B lymphocytes. Using two-photon microscopy, we further examined NK cell behavior within infected lymph nodes. NK cells were rapidly recruited to sites of infection but did not form stable clusters or prolonged contacts with infected cells. Nevertheless, NK cell depletion resulted in increased numbers of infected cells, indicating that NK cells contribute to the control of acute MHV68 infection despite the absence of detectable long-lasting interactions with infected cells. Together, our findings provide a single-cell view of acute gammaherpesvirus infection and innate immune control within lymph nodes in vivo. These data refine our understanding of how type I IFN responses and NK cells restrict early gammaherpesvirus spread and shape infection dynamics within lymphoid tissues. Author SummaryCertain viruses can remain in the body for life and cause little harm in healthy individuals. However, when the immune system is weakened, these infections can lead to cancer or other life-threatening diseases. To study human gammaherpesviruses within the living body, scientists often use a closely related mouse virus to understand how the immune system controls these infections. In this study, we tracked virus-infected cells within lymph nodes, important sites of the immune responses. Using a fluorescent virus together with advanced imaging techniques, we visualized infected cells directly in intact tissues. We found that type I interferons, a key component of the early antiviral defense, strongly limited the number of infected cells. Mice that could not respond to type I interferons developed substantially larger infections. We also investigated the role of natural killer cells, immune cells that provide rapid protection against viral infections. Although these cells quickly accumulated at sites of infection, they rarely formed prolonged contacts with infected cells. Together, our findings provide a detailed view of how innate immune defenses restrict gammaherpesvirus infection within lymph nodes. By revealing how early immune responses limit viral spread, this work improves our understanding of mechanisms that protect against severe herpesvirus-associated disease.

immunology↗

bioRxiv2025

Integrative spatial and multi-omic profiling in bladder cancer links L1 retrotransposition to extrachromosomal DNA, genomic instability, and viral mimicry response

Bladder cancer is one of the most frequent cancers and shows high recurrence rates. Despite recent advances, key knowledge gaps remain in understanding the molecular mechanisms of disease progression, which would support the development of early detection methods and effective personalized treatments. We apply integrated multi-omics and spatial analyses in a cohort of 49 bladder cancer patients to comprehensively profile genetic, epigenetic, transcriptomic, and spatial features of bladder cancer, alongside cell-free DNA blood analysis. Combining low-pass whole-genome cell-free DNA sequencing, Oxford Nanopore long-read tumor DNA sequencing, RNA-sequencing, and spatial transcriptomics, we provide insights into molecular alterations driving bladder cancer. We show frequent somatic LINE-1 (L1) insertions, with up to more than 500 insertions per tumor. We find that L1 insertions are active and occur early in bladder cancer development. We link aberrant somatic L1 insertion in bladder cancer with downstream genomic rearrangements and chromosomal instability, with an excess of structural variants and extrachromosomal DNA (ecDNA) in patients with particularly high L1 counts. By detecting ecDNA within tissue architecture using spatial transcriptomics, we identify the localization of ecDNA to distinct spatial clusters with differential expression of APOBEC3B and immune response pathways. These results, combined with replication timing analysis and gene set enrichment analysis (GSEA), offer evidence for the previously hypothesized viral mimicry response to L1 retrotransposition, mediated via APOBEC3B-editing, the cGAS-STING pathway, and RIG-I and MDA5 responses.

cancer biology↗

bioRxiv2024

Test-retest reliability of auditory MMN measured with OPM-MEG

In this paper, we report results from an investigation of auditory mismatch responses as measured by magnetoencephalography (MEG) based on optically pumped magnetometers (OPM). Specifically, as part of a quality control study, we examined the reliability and validity of auditory mismatch negativity (MMN) recordings, obtained with a newly installed OPM-MEG system. Based on OPM-MEG data from 30 healthy volunteers, measured twice with an established auditory MMN paradigm with frequency deviants, we examined the following questions: First, we focused on construct validity and examined whether OPM-MEG measurements of MMN responses (in terms of event-related fields, ERFs) were qualitatively comparable to previous MMN findings from studies using EEG or MEG based on superconducting quantum interference devices (SQUIDs). In particular, we examined whether significant MMN responses measured by OPM-MEG occurred in a comparable time window and showed a similar topography as in previous EEG/MEG studies of MMN. Second, we quantified test-retest reliability of MMN amplitude and latency over two separate measurement sessions. The results of our analyses show that MMN responses recorded with OPM-MEG are in good agreement with previously reported MMN results in terms of timing and topography. Furthermore, the comparison of group-level MMN topographies and timeseries shows excellent consistency across the two measurement sessions. Our quantitative test-retest reliability analyses at the sensor level indicate good reliability for MMN amplitude, but poor reliability for MMN latency. Overall, our findings suggest that OPM-MEG measurements of auditory MMN (i) are comparable to results from EEG and SQUID-based MEG and (ii) show good test-retest reliability for amplitude measures at the sensor level. Notably, these results were achieved in an "out of the box" state of the OPM-MEG system, shortly after installation and without further optimisation. The reason for the insufficient reliability for MMN latency we observed is currently under investigation and represents an important target for future improvements.

neuroscience↗

bioRxiv2024

Herpes Simplex Virus Assembly and Spread in murine skin after infection from the outside

Herpes simplex viruses (HSV) cause many skin diseases, particularly in immunocompromised patients. HSV-1 infection of murine skin recapitulates many aspects of human pathology. However, many protocols rely on mechanical or enzymatic skin disruption to induce lesions, although this can alter skin homeostasis and prime antiviral inflammation before inoculation. To investigate the initial events following HSV-1 primary skin infection before the onset of symptoms, we developed a novel murine ex vivo explant model using gentle depilation but no further scarification and infected keratinocytes from the outside with minimal tissue damage. Two-photon microscopy studies showed that HSV-1 spread exclusively in the epidermis. The infection centers increased in number and size over time and contained hundreds of infected keratinocytes. We investigated the HSV-1 spread at the cellular level, using reporter strains with fluorescently-tagged capsid protein VP26, and monitored the formation of nuclear capsid assembly sites, nuclear capsid egress, and the recruitment of the inner tegument protein pUL37GFP, the outer tegument protein VP11/12GFP, and the envelope protein gDGFP to cytoplasmic capsids. By electron microscopy, the skin appeared intact, and keratinocytes contained many nuclear capsids, primary virions in the nuclear envelope, cytosolic membrane-associated capsids, and enveloped virions. Our protocol provides a robust and reproducible approach to investigate the very early events of HSV-1 spread in the skin, to characterize the phenotypes of HSV-1 mutants in terminally differentiated skin tissues, and to evaluate potentially antiviral small molecules in a preclinical ex vivo infection model. IMPORTANCEThis study describes a novel murine ex vivo skin explant model to investigate early events in HSV-1 infection without causing significant tissue damage. To infect from the outside, via the apical keratinocytes, this method relies on gentle depilation, which maintains skin integrity. HSV-1 spread exclusively within the epidermis, with infection centers growing over time and involving hundreds of keratinocytes. Using advanced microscopy techniques, we tracked HSV-1 spread at the cellular level and intracellular assembly of all intermediate virus structures. This model offers a valuable tool for studying the initial stages of HSV-1 infection, assessing viral mutant phenotypes, and testing antiviral compounds in a more physiological context to provide critical insights into HSV-1 pathogenesis and therapeutic strategies.

microbiology↗

bioRxiv2023

Feasibility of improving manufacturability based on protein engineering

While bioactivity and a favorable safety profile for biotherapeutics is of utmost importance, manufacturability is also worth of consideration to ease the manufacturing process. Many biotherapeutics are typically expressed in mammalian cells. Process-related impurities or biological impurities like viruses and host cell proteins (HCP) are present in the harvest which have mostly acid isoelectric points and need to be removed to ensure safety for the patients. Therefore, during molecule design, an isoelectric point of the target molecule should preferably differ sufficiently from the isoelectric points of the impurities to enable an efficient and straightforward purification strategy. In this feasibility study we have evaluated the possibility to improve manufacturability by increasing the isoelectric point of the target protein. We have generated several variants of a GLP1-receptor-agonist-Fc-domain -FGF21 fusion protein and demonstrate that the critical anion exchange chromatography step can be run at high pH values with maximal product recovery theoretically allowing removal of HCP and viruses. Addressing the isoelectric point can be useful for an efficient process for removing HCP and viruses and this topic should be considered early in the research phase to ensure that other important molecule properties, e.g. safety, efficacy and expression yield are not impacted.

bioengineering↗

bioRxiv2023

Incorporating uncertainty within dynamic interoceptive learning

Interoception, the perception of the internal state of the body, has been shown to be closely linked to emotions and mental health. Of particular interest are interoceptive learning processes that capture associations between environmental cues and body signals as a basis for making homeostatically relevant predictions about the future. Here we extended an interoceptive Breathing Learning Task (BLT) to incorporate continuous measures of prediction certainty, and tested its application using a Rescorla Wagner (RW) associative learning model. Sixteen healthy participants completed the continuous version of the BLT, where they were asked to predict the likelihood of breathing resistances. The task was modified from a previous version and required continuous, rather than binary predictions, in order to include a more precise measure of prediction certainty. The RW model was used to fit a learning rate to each participants continuous and binarised predictions, and was additionally extended to test whether learning rates differed according to stimuli valence. The empirical task data demonstrated excellent replicability compared to previously collected data using binary predictions, and the continuous model fits closely captured participant behaviour at the group level. The model extension to estimate different learning rates for negative (i.e. breathing resistance) and positive (i.e. no breathing resistance) trials indicated that learning rates did not significantly differ according to stimuli nature. Furthermore, examining the relationship between estimates of prediction certainty and learning rates with interoceptive and mental health questionnaires demonstrated that fatigue severity was related to both prediction certainty and learning rate, and anxiety sensitivity was related to prediction certainty. The updated task and model show promise for future investigations into interoceptive learning and potential links to mental health.

neuroscience↗